Installing Bioconductor 1.5 on R 2.0 for OS X
Stefano, I have R 2.0.0 and am working with BioC 1.5, so far from source. I really don't want to compile from source if I can help it, but I can try setting up per the FAQ. It sounds like I should not use fink binaries for g77, and that I can fairly easily change. I attached a text file of the status/error messages I have gotten so far in the BioC/DNAcopy installs. Thanks for the quick response... Mike ---
stefano iacus wrote:
On Nov 2, 2004, at 11:11 PM, Michael Redmond wrote:
I have a working version of R 2.0 with option packages installed on an OS X 10.3.5 system. Option packages were installed with install.binaries option and that seemed to work. Install using sources failed.
hi Michael, what exactly fails? You should set up the system as it is explained in the FAQ and g77 is one issue. Are you using the getbioC script ? BioC 1.4 needs R 1.9.1 and 1.5 (to be released) needs R 2.0.0. You cannot use bioc 1.5 with 1.9.x
I tried installing bioconductor from sources and got mixed results (at best). Some packages failed to install (annotate, graph, Rgraphviz and maybe XML and possibly others). I also need to install arrayCGH to get DNAcopy. That uses the g77 compiler and failes with a mismatch of gcc library versions. I have g77 from fink.
I strongly suggest you one of the two options 1. build R from scratch eventually using fink stuff 2. remove any fink stuff, and use the cran binary of R 2.0.0.
Is there a install.binary option for bioconductor and some of the bioconductor contributed packages (specifically arrayCGH)? If not now, when (if ever). If never, I may need some help to fix compile errors trying from source.
you should report the error logs to let us to help with these. I'm currently testing the build of BioC 1.5 using getBioC. I'll put results here and on the bioc-related lists. stefano
I am working on this for an Apple 4 node XServe to see if it can be used under the iNquiry portal for R/Bioconductor applications. Thanks Mike Redmond UW-Madison Statistics
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-------------- next part -------------- [1] "Installation complete"
widgetTools version 1.4.7
DynDoc version 1.5.0
tkWidgets version 1.5.20
Biobase version 1.5.0
affydata version 1.4.0
affy version 1.5.8
affyPLM version 1.2.5
genefilter version 1.5.0
Biostrings version 1.0.0
matchprobes version 1.0.12
multtest version 1.5.2
annaffy version 1.0.11
gcrma version 1.1.1
makecdfenv version 1.4.8
Ruuid version 1.5.0
geneplotter version 1.5.0
edd version 1.5.0
ROC version 1.0.13
marray version 1.5.25
RMAGEML version 2.1.0
siggenes version 1.2.11
vsn version 1.5.0
hgu95av2cdf version 1.4.3
hgu133acdf version 1.4.3
hu6800cdf version 1.4.3
GO version 1.6.5
KEGG version 1.6.5
hgu95av2 version 1.6.5
rae230a version 1.6.5
hsahomology version 1.6.5
xlahomology version 1.6.5
zebrafish version 1.6.5
xenopuslaevis version 1.6.5
hu6800 version 1.6.5
hgu95av2probe version 1.0
hu6800probe version 1.0
rae230aprobe version 1.0
XML version 0.95-6
XML version 0.95-6
SparseM version 0.52
XML version 0.95-6
xtable version 1.2-4
statmod version 1.1.0
sma version 0.5.14
limma version 1.8.6
XML version 0.95-6
pamr version 1.22
fibroEset version 1.0
golubEsets version 1.0
Packages that were not updated:
annotate
annotate
graph
Rgraphviz
annotate
You have downloaded a default set of packages.
If you wish to see other download options, please go to the URL:
http://www.bioconductor.org/faq.html#getBioC
There were 14 warnings (use warnings() to see them)
warnings()
Warning messages: 1: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 3: Package annotate version 1.5.1 suggests genefilter Package annotate version 1.5.1 suggests XML version >= 0.92-2 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions, ... 4: Installation of package annaffy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 5: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 6: Package annotate version 1.5.1 suggests XML version >= 0.92-2 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions, ... 7: Installation of package SparseM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 8: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 9: Package graph version 1.5.0 suggests SparseM version >= 0.36 Package graph version 1.5.0 suggests XML in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions, ... 10: Package Rgraphviz version 1.5.0 depends on graph in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions, ... 11: Installation of package geneplotter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 12: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 13: Package annotate version 1.5.1 suggests XML version >= 0.92-2 in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions, ... 14: Installation of package pamr had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) -----
getBioC("arrayCGH")
Running getBioC version 1.2.68.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Attempting to download DNAcopy from http://www.bioconductor.org/repository/release1.5/package/Source" [1] "Download complete." [1] "Installing DNAcopy" * Installing *source* package 'DNAcopy' ... ** libs g77 -fno-common -g -O2 -c changepoints.f -o changepoints.o g77 -fno-common -g -O2 -c prune.f -o prune.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c rshared.c -o rshared.o gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o DNAcopy.so changepoints.o prune.o rshared.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem -lcc_dynamic -framework R ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist ld: can't locate file for: -lfrtbegin make: *** [DNAcopy.so] Error 1 ERROR: compilation failed for package 'DNAcopy' Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download rmutil from http://www.bioconductor.org/repository/lindsey/" [1] "Download complete." [1] "Installing rmutil" * Installing *source* package 'rmutil' ... ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c cutil.c -o cutil.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c dist.c -o dist.o g77 -fno-common -g -O2 -c gettvc.f -o gettvc.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c romberg.c -o romberg.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c toms614.c -o toms614.o gcc -bundle -flat_namespace -undefined suppress -o rmutil.so cutil.o dist.o gettvc.o romberg.o toms614.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist ld: can't locate file for: -lfrtbegin make: *** [rmutil.so] Error 1 ERROR: compilation failed for package 'rmutil' Note: Package rmutil not found in any known repository. Note: Package repeated not found in any known repository. Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download rmutil from http://www.bioconductor.org/repository/lindsey/" [1] "Download complete." [1] "Installing rmutil" * Installing *source* package 'rmutil' ... ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c cutil.c -o cutil.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c dist.c -o dist.o g77 -fno-common -g -O2 -c gettvc.f -o gettvc.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c romberg.c -o romberg.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c toms614.c -o toms614.o gcc -bundle -flat_namespace -undefined suppress -o rmutil.so cutil.o dist.o gettvc.o romberg.o toms614.o -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin -lg2c -lSystem ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist ld: warning -L: directory name (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist ld: can't locate file for: -lfrtbegin make: *** [rmutil.so] Error 1 ERROR: compilation failed for package 'rmutil' ** Removing '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/rmutil' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/rmutil' [1] "Attempting to download aCGH from http://www.bioconductor.org/repository/release1.5/package/Source" [1] "Download complete." [1] "Installing aCGH" * Installing *source* package 'aCGH' ... ** R ** data ** demo ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'aCGH' Formats: text html latex example aCGH text html latex example aCGH.process text html latex example aCGH.read.Sprocs text html latex example aCGH.test text html latex example clusterGenome text html latex example colorectal text html latex example computeSD.func text html latex find.genomic.events text html latex find.hmm.states text html latex example findAber.func text html latex findAmplif.func text html latex findOutliers.func text html latex findTrans.func text html latex gainLoss text html latex example heatmap text html latex example human.chrom.info.Jul03 text html latex impute.lowess text html latex example mergeFunc text html latex plotFreqStat text html latex example plotGenome text html latex example plotHmmStates text html latex example plotSummaryProfile text html latex example states.hmm.func text html latex summarize.clones text html latex example * DONE (aCGH) chmod: /Library/Frameworks/R.framework/Versions/2.0.0/Resources/library/R.css: Operation not permitted [1] "Installation complete"
DNAcopy version 1.1.0
aCGH version 1.1.4
rmutil version 1.0
rmutil version 1.0
Packages that were not updated:
repeated
Warning messages:
1: Installation of package DNAcopy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
2: Installation of package rmutil had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3:
Package repeated version 1.0 depends on rmutil
in: resolve.depends(pkgInfo, repEntry, force, lib = lib, searchOptions = searchOptions,
4: Installation of package rmutil had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)